Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59 (characterized)
to candidate Echvi_3894 Echvi_3894 Transcriptional regulator/sugar kinase
Query= CharProtDB::CH_002679 (303 letters) >FitnessBrowser__Cola:Echvi_3894 Length = 291 Score = 95.9 bits (237), Expect = 1e-24 Identities = 78/272 (28%), Positives = 127/272 (46%), Gaps = 42/272 (15%) Query: 4 GFDIGGTKIALGVFDSGRQLQWEKRVPTP-RDSYDAFLDAVCELVA-----EADQRFGCK 57 G DIGGT I G+ G ++ ++ +PTP ++ + L + + +A E D Sbjct: 9 GLDIGGTSINAGIMKDGELIE-KREIPTPSQEPQEVILSTIADFIASYFSHEID------ 61 Query: 58 GSVGIGIPGMPETEDGTLY-AANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWD 116 +GIGIPG+ + E G +Y N+PA + L+ L L++ V ++NDANCFAL E Sbjct: 62 -GIGIGIPGLVDAEKGIVYNLENIPAFNKVALKDYLERTLEKPVYINNDANCFALGEYKF 120 Query: 117 DEFTQYPLVMGLILGTGVGGGLIFNGKPITGKSYITGEFGHMRLPVDALTMMGLDFPLRR 176 ++ ++G+ LGTG+G G+I NG+ G GE+G + + +F Sbjct: 121 GGANKHRHMVGITLGTGIGTGVITNGELYPGFLCGAGEWG-------GVPYLDSNF---- 169 Query: 177 CGCGQHGCIENYLSGRGFAWLYQHYYHQPLQAPEIIALYDQGDEQARAHVERYLDLLAVC 236 ENY S + F L+ A ++ A +GD++A Y + Sbjct: 170 ---------ENYCSSKFFRKLHH------TTAKKLAAKAAEGDQEALKLFYEYGTHIGNL 214 Query: 237 LGNILTIVDPDLVVIGGGLSN-FPAITTQLAD 267 + IL P+ +VIGG + FP + L + Sbjct: 215 IKYILFTYAPEAIVIGGSIRKAFPYFSKGLKE 246 Lambda K H 0.323 0.143 0.451 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 209 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 303 Length of database: 291 Length adjustment: 26 Effective length of query: 277 Effective length of database: 265 Effective search space: 73405 Effective search space used: 73405 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory